Contacts of the helix formed by residues 77 - 87 (chain B) in PDB entry 1VYH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 77 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B GLY 3.9 7.0 - - - +
76B ASP* 1.3 77.4 - - - +
78B THR* 1.3 66.3 + - - +
79B ARG* 3.4 19.8 + - - +
80B HIS* 3.0 33.3 + - + +
81B VAL* 3.0 22.0 + - - +
102B VAL* 3.7 6.2 - - - +
105B ASN* 4.0 19.1 - - - +
106B ASN* 3.5 21.1 - - - +
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Residues in contact with THR 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA* 3.0 25.5 + - - +
77B THR* 1.3 72.2 - - - +
79B ARG* 1.3 62.6 + - - +
81B VAL 3.4 0.2 + - - -
82B LEU* 3.0 30.2 + - - +
102B VAL* 3.7 13.9 - - + +
103B GLY* 4.7 2.7 - - - -
106B ASN* 2.8 33.4 + - - +
114B VAL* 4.3 7.4 - - + +
117B GLY* 4.0 5.2 - - - -
118B ILE* 3.9 29.8 - - + +
121B ILE* 3.8 17.0 - - + +
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Residues in contact with ARG 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 2.4 38.2 + - - +
9B ALA* 3.6 11.9 - - - +
11B ILE* 3.3 23.6 + - - +
13B HIS* 2.8 65.4 + - + +
77B THR* 3.1 11.8 + - - +
78B THR* 1.3 78.1 - - - +
80B HIS* 1.3 62.4 + - + +
82B LEU* 3.3 10.6 - - - +
83B TRP 3.2 17.0 + - - -
106B ASN* 4.9 3.1 - - - +
108B GLU* 5.9 0.8 + - - -
109B ASN* 5.6 4.8 - - - +
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Residues in contact with HIS 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B HIS* 3.2 38.8 + - - -
15B ALA* 3.2 38.3 - - + +
24B TRP* 3.9 4.5 - + + -
75B GLY 4.6 4.9 - - - -
76B ASP* 3.2 27.9 + - - +
77B THR* 3.0 42.1 + - + +
79B ARG* 1.3 77.0 - - + +
81B VAL* 1.3 64.8 + - - +
83B TRP* 3.1 4.7 + - - +
84B ARG* 2.9 28.0 + - - +
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Residues in contact with VAL 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 4.9 8.1 - - + -
46B GLY* 4.0 13.9 - - - +
76B ASP* 3.8 7.2 - - + +
77B THR 3.0 15.0 + - - +
78B THR 3.9 2.0 - - - +
80B HIS* 1.3 72.3 - - - +
82B LEU* 1.3 69.7 + - - +
84B ARG* 3.3 30.5 + - - +
85B LEU* 2.9 42.1 + - + +
102B VAL* 3.9 26.5 - - + -
121B ILE* 4.0 18.8 - - + -
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Residues in contact with LEU 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ALA 3.9 14.6 - - - +
10B ALA* 3.9 22.2 - - - +
12B PRO* 4.1 10.1 - - + -
78B THR 3.0 27.4 + - - +
79B ARG* 3.3 10.3 - - - +
81B VAL* 1.3 75.5 - - - +
83B TRP* 1.3 52.4 + - - +
85B LEU* 2.7 30.0 + - - +
86B LYS* 2.7 29.2 + - - +
117B GLY 4.4 4.3 - - - +
120B ALA* 4.3 10.3 - - + +
121B ILE* 3.6 37.7 - - + +
124B LEU* 4.3 13.8 - - + +
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Residues in contact with TRP 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 3.9 15.4 - - + +
13B HIS* 3.4 33.7 - - - +
14B ALA* 3.4 34.5 - - + +
24B TRP* 4.3 11.0 - + - -
25B MET* 4.4 16.2 - - + -
28B HIS* 3.7 22.0 - + - -
79B ARG 3.2 1.4 + - - +
80B HIS 3.1 8.8 + - - +
82B LEU* 1.3 78.5 - - - +
84B ARG* 1.3 58.6 + - - +
86B LYS* 3.2 2.3 + - - -
87B ASN* 2.7 80.1 + - + +
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Residues in contact with ARG 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TRP* 3.5 27.6 - - + -
28B HIS* 3.6 18.2 - - - +
31B PHE* 4.5 0.4 - - - -
45B VAL* 5.5 2.0 - - - +
46B GLY 3.4 16.8 + - - +
71B PHE* 3.2 24.7 + - - +
73B ILE* 3.4 24.5 - - - +
76B ASP* 2.8 27.5 + - - -
80B HIS 2.9 17.2 + - - +
81B VAL* 3.4 19.4 + - - +
83B TRP* 1.3 75.5 - - - +
85B LEU* 1.3 64.8 + - - +
87B ASN 3.2 11.3 + - - -
88B GLY 3.5 1.2 + - - -
89B GLU* 2.7 65.4 + - - +
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Residues in contact with LEU 85 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B VAL* 3.8 31.9 - - + -
81B VAL* 2.9 38.7 + - + +
82B LEU* 2.7 13.0 + - - +
84B ARG* 1.3 73.6 - - - +
86B LYS* 1.3 61.1 + - - +
87B ASN 3.4 0.3 + - - -
88B GLY* 3.5 7.3 + - - -
89B GLU* 3.8 19.9 + - + +
90B LEU* 3.7 44.3 - - + +
121B ILE* 4.1 23.6 - - + +
124B LEU* 3.9 10.3 - - + -
125B ILE* 4.1 15.9 - - + -
128B ARG* 4.7 2.8 + - - -
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Residues in contact with LYS 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B PRO* 4.5 27.1 - - + +
82B LEU* 2.7 25.1 + - - +
83B TRP* 3.6 9.4 - - - +
85B LEU* 1.3 75.1 - - - +
87B ASN* 1.3 64.3 + - - +
88B GLY 3.3 3.5 + - - -
91B GLU* 5.6 1.7 - - - +
124B LEU* 3.8 30.9 - - + +
128B ARG* 3.3 35.2 + - - +
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Residues in contact with ASN 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B HIS* 3.6 14.6 + - - +
32B VAL* 4.4 5.9 - - - +
83B TRP* 2.7 86.9 + - + +
84B ARG 3.2 5.3 + - - -
86B LYS* 1.3 79.3 - - - +
88B GLY* 1.3 56.7 + - - +
91B GLU* 5.2 0.4 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il